From perk description it is not clear to me if having a perk in list gives you additional bonus in probability modifiers, or it's simple skills percent bonus.

E.g. Ranger gives you description that with this perk you are more likely to have special encounters, and gives you a 15% bonus on Outdoorsman skill. Is it equivalent to just increase Outdoorsman skill the same amount to have the same effect?

Other example: Medic perk gives you 10% to First Aid and Doctor skills. Same as simply increasing this skills spending the skill points?

Simply put, does game actually check against having/not having specific perk? E.g. is just having a 80% speech, or having 80% speech with a Speaker perk (40% base + 40% with perk) will result in same checks or not?

I mean it's obvious that perk checks are done to perks that does not give you skill bonus points (at least that you can see), like Explorer or Kama Sutra Master. But do percentage-bonus type perks (like Speaker in example above) give any additional checks (not always of course) except ones that apply to skill value?

1 Answer
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When the game is checking a specific skill's score, having bonus points in that skill from having a related perk are treated exactly the same as having invested discretionary points from leveling directly into that skill. However, the game does, in certain circumstances, check for specific perks.

If you need a score of 90% in Doctor to open a specific dialog choice, it doesn't matter if you have 80% from points invested and 10% bonus from the Medic perk, or if you have 100% invested directly from skill points earned.

Similarly, calculations based off of skill points (such as chance-to-hit with a weapon) are based off of your current skill point value, regardless of whether those skill points are added by perks or not.

There are some dialog options that are only available if you have a specific perk, though. In these cases, having the perk does matter, as it is looking specifically to see if you have the given perk (possibly in addition to having a specific skill score). These dialog options can apply to perks that ostensibly only provide a flat bonus to one or more skills.

As a specific example, the quest "Take care of officer Jack" can be completed by talking Jack out of it, which requires either a Speech score of 80%, or the Speaker perk (which normally only raises your Speech skill by 20%/40%, depending on which patch version you have).